The Genius and The SO
by Kajos
Summary: Sheppard/McKay AU John never had a family. He was military, raised from birth knowing what his future held. He was destined protect and sleep with some genius scientist for his country. What he never expected was to love and be loved. SLASH
1. Chapter 1

Disclaimer: I don't own Stargate Atlantis, any of its technologies, settings, characters or plot lines and I'm only really borrowing one or two settings and characters for this anyway. Well for now. Who knows what will happen later.

Summary: John never had a family. He was military, raised from birth knowing what his future held. He was destined by politics to live with, protect and sleep with some genius scientist for the good of his country and all the civilians. What he never expected was to love or be loved.

Rating: M for slash

Kajos: Also a big thank you to cookie62 for being Beta for this.

JS had two years to wallow, two years to isolate himself from the world and his duty. After Nancy there had been a lot of talk of change, of reassignment and a review of his status. As it was he had been black marked and placed on helicopter taxi for two years. It was embarrassing, he was twenty, single and in Antarctica. Until the orders came through that an assignment had been found for him; news that he did have a life still. He was military and he was a trained special ops agent. Picked at the age of six with a high IQ and great potential he had been fast tracked into the select program that was reserved for this work. He had been introduced to Nancy at 14, they had had a year to get to know each other before they were married and Nancy was sent off on her first project. JS had gone with her, to protect her, as was his purpose.

He had failed. A year later it was discovered that Nancy had contracted a disease, it had made her sterile and resulted eventually a year and a half later in her death. Medical or not it was JS's fault. He should have at least made sure in the year that she had conceived a child; he had thought that they had time though. The letter was absolution. A second chance he had though impossible. Special ops were paired with geniuses at the age of ten; they chose special ops at the age of six when geniuses were selected from school to be certain that the numbers were correct. They were introduced at 14, married anywhere from six months to two years later depending on physical development and when they were sent on projects.

McKay though had gone through three SOs and sent them back. He was now twenty two and alone. Of course without special ops he was refused a place on any project. It just wasn't safe with his genes. The world was desperately streamlining population. In the early 21st century it had been realized that soon the world's population would become too large to manage. Countries everywhere had introduced various methods of population control. The USA and much of Europe had begun forced sterilization. Only those deemed to have superior genes were allowed to procreate. Only the top 5% of people in any area from field workers to politicians were allowed to procreate, those though were expected to have more children than was once the norm. To compensate for the effect of large families the civil service, military and education systems had been reformed. A pairings first child was automatically placed in the military where they were raised with the imbedded primary purpose to defend civilians and the country. The second child remained with the parents and third went into the civil service, trained from the start to be postal workers, lawyers, politicians, police or anything else the government required of them.

Other children if the parents wished could be given to sterilize couples the government deemed suitable. The system had pulled the world back from collapse but it had also cause controversy and war. Throughout the war geniuses, the best of the best were deemed as extremely valuable breeding stock that must be protected and utilized by each country. That was JS's purpose, to defend the countries best assets, the highly intelligent. He didn't know anything about this McKay other than the fact that he required an SO immediately and he was the only appropriate candidate.

JS landed in Colorado five hours after informing his CO in Antarctica he was leaving. A tired looking Colonel met him off the plane; he had to be at least 35. He checked his uniform and was surprised to see that the man was special ops and held a command position. It was unusual but not unheard of, normally it was consider risky, as you were required to protect your partner above all else.

"Welcome to Colorado Springs Major JS. I'm very pleased to see you."

"Colonel" He said and saluted. The man waved him off.

"Come on, I want to get you to the mountain as soon as possible. The good doctor is driving everyone insane."

"Really?" The Colonel looked JS up and down.

"I've read your file Major, you aren't one to follow orders blindly, you keep to your directive but unlike some you don't bow to the whims of civilians in your care. The last two SO's McKay has had were straight as arrows, boot lickers. They didn't do their jobs properly allowing McKay to get away with things he should never have been allowed to even consider because he told them to. There were five candidates this time. As the ranking SO I was required to make a choice, normal procedure would have been to contact the other four and give McKay the choice, you have a black mark after all. I didn't though. You were the only candidate that has any chance of keeping hold of McKay." The Colonel explained without hesitation. JS considered it. Nancy had often been care free with her safety forcing JS to act in her best interest even if it was against her wishes. "Now if you don't mind the car is waiting as is your scientist."

The journey passed in silence as JS catalogued his surroundings, noting every detail. He was already back in SO mode which Colonel JO next to him seemed to approve of. They arrived at the Cheyenne Mountain complex without issue. But JS was confused as they changed from the first elevator to a second that went down further than the lowest level of the known base.

"You are now entering Stargate Command. Better known as the SGC. We'll put you through the intro videos tomorrow, after you have met McKay. Just be aware that this is all above top-secret clearance. As far as any one you meet outside this base is concerned no matter what they tell you, this place does not exist unless, I or another confirmed senior officer of this command gives you clearance."

"Sir, why did McKay get rid of his first SO?" The Colonel looked at him.

"Because he was an idiot." The Colonel stated simply. This made JS gulp, SO's were the most intelligent members of the military, some were geniuses in their own right.

"Exactly how intelligent is McKay?" He tentatively asked. Nancy had only scrapped into the genius program.

"He's the smartest in his field they've ever had through the Genius academy." JS was stunned, geniuses that smart were celebrities yet he had never heard of the man in his life. "Don't worry, we snapped him up very quickly at the SGC making sure he was never known. His intelligence is as big a secret as this base." JO seemed to read his mind.

The elevator finally came to a halt and The Colonel exited followed by JS.

"Jack!" came a happy voice from down the corridor. JS stiffened as the young sandy haired man headed towards them down the corridor. He was clearly Colonel JO's partner, having used his first name rather than the initials that all military used both with one another and civilians. The man's face instantly brightened at his partner's presence.

"Danny." He said softly as the blonde reached them. "This is the new SO for McKay." He said taking the other man's hand. 'Danny' gave him a look over then held out a hand shocking JS to the core. He was a civilian.

"Nice to meet you, I'm Doctor Daniel Jackson. I wish you all the best with Dr McKay. He's…one of a kind. May I ask your name?" JS tentatively took his hand.

"Um…thank you. I'm Major JS."

"JS, excellent. Now I need to return to work. I'll see you later Jack?"

"Of course. I'll see you at six for dinner when you will be done for the day."

"Jack I have a lot of work to get through, I won't be that late, just this once."

"Ah! Six Danny. You're still recovering from that mission and none of that work has to be done tonight. It will all wait till tomorrow." The doctor acquiesced and left.

"I apologize, Daniel believes in military integration." JS nodded in understanding. He had never actually met an integrationist before though. He had always been aware though of those that disagreed with the fact the military unlike the civil service were completely segregated from the rest of society with separate shops, bars, restaurants and even a system of naming that separated them from civilians. Though JS could see their point, the military needed to be separate. They could not defend civilians if they were equal. Civilians always came first. If they made a request of you, you fulfilled it. It was not as though the military did not have rights they simply had a duty as well.

As they passed through the corridors JS quickly realized the unusually high prominence of SO's in the base. They seemed to make up about 50% of the military, this meant that the scientists and academics he saw with them and wandering the corridors alone were almost all Geniuses. What the hell was this place?

As they approached the lab JS could hear someone yelling.

"YOU INCOMPETENT BUFFONS! WHY MUST YOU TOUCH THINGS! I THOUGHT I BANNED YOU ALL FROM THE LAB! YOU'RE MAKING THE PLACE MORE DANGEROUS WITH YOUR INCOMEPTENCE!" The Colonel stopped and sighed as a small group of SOs left the room looking rather afraid.

"Those would be the dulcet tones of one Dr McKay." JS gulped again. McKay seemed to make him do that a lot and he hadn't even met him yet. "Don't worry," The Colonel said pushing him forward, "he doesn't bite unless you're withholding caffeine." JS slowly walked to the door and stepped inside.

"Whoever this one belongs to can you please teach him English? I told you all to get out!" McKay said. He was broad shouldered with a trim figure and a mat of brown hair on his head. His blue/grey eyes burned with annoyance but on first sight JS could see the slight bags under his eyes the slump in his shoulders and the twitchiness that suggested he'd been running on Caffeine for far too long. His brain instantly slipped into protector. He was pissed that no one had done something before now about putting a stop to this. "Hello? Anyone in there?" The Doctor said waving a hand in front of his face. "I told you to _leave_."

"Fine, I'll leave." The Doctor smiled. "As long as you come with me."

"What?" McKay asked wondering if this was a joke, he had important work to be doing.

"You heard me. Until you leave I am going to sit here and touch experiments and mess with things I shouldn't."

"And who would you be exactly?" McKay seethed.

"Major JS, Special Ops. Pleased to meet you." McKay exploded at that point.

"COLONEL!" The senior officer winced as he stepped into the room. "I should have known! I told you I explicitly did not want another watch dog." The military man straightened his back and starred back at the scientist.

"It's the law McKay and you know it."

"Oh, please. I am not procreating on the whim of some government policy. It's bad enough they force those operations on us."

"The Major is here for your protection as much as for procreation and you have already been told that you are free to make use of a surrogate as long as you donate your own genetics."

"How is he going to protect me? Is that thing on top of his head going to leap at the enemy?" JS was fed up now.

"I'm a fully trained SO, first in my class."

"Well that's good for you but I don't need a watch dog telling me how great I am."

"That's fine with me." JS scoffed. McKay starred at him indignantly.

"What's that supposed to mean?"

"Well, from what I've seen your just loud, that doesn't make you smart just annoying. Plus you obviously not smart enough to take care of yourself, it's been what eight hours since you last ate and you're certainly not getting more than a few hours sleep a night." The doctor starred at him in horror. "And I would say you need the sleep since you haven't spotted the obvious flaw in that calculation." He said pointing to a black board full of scribbled mathematics. McKay turned around and looked at it for a moment.

"No, those calculations are fine." JS just stood and walked to the board. He rubbed out a small section replaced it and then work through with the change. McKay considered for a moment, while Colonel JO grinned in satisfaction. He knew this would work.

"Now I think it's time we left and went somewhere a little less public for you to shout at me." After that the major just stood and waited in the doorway. After a few moments of stuttering McKay followed him out the door with JO bringing up the rear. They headed for the Doctors office as the closest place that was appropriate.

"Thank you so much for embarrassing me in front of my team Major, it really endeared me to you." Sarcasm poured out of the doctor's tone.

"I apologize but it was the only way to get you to listen." JS said seriously. "I'll be honest with you Dr McKay; this is not where I expect to be in life. You should know that I lost my first Genius. I allowed her to get a tropical disease because I failed to get her to see a doctor quick enough. She died. I never thought I'd get the chance to do anything important again. I am one of the best out there and I won't let someone I'm responsible for hurt themselves. As far as I'm concerned you are now in my care, whether you like it or not, you are going to eat and sleep more."

The Colonel cleared his throat pulling McKay's attention to him. "Do you accept Major JS as you're SO on a trial basis?"

"On a trial basis only, this is not permanent by any means." JO just nodded and left the pairing alone.

"Well, I suppose you should call me Rodney. What does JS stand for?"

"John Sheppard."

"Is John an assigned name or did your parents actually name you?" John shrugged.

"I thought you were Dr M R McKay anyway. What's the M for?"

"Meredith, but I order you never to reveal that fact." John burst out laughing.

"Meredith….Meredith? That's a girl's name!"

"Says the man who has initials for a name." John didn't stop laughing for a few minutes as Rodney snarked.

"Right, I think first stop is the commissary, then bed."

"Oh! You are not sleeping with me. I don't care what the politics say I'm not some stud to rut with anything that comes along with a hole."

"I wasn't even thinking it and anyway." He lowered his voice significantly "You're the hole here not me." Rodney just looked shocked and indignant, a look this John seemed to be causing a lot as the Major walked out the door.

After John had made sure that Rodney had eaten properly he stood and cleared both trays before returning to the table.

"Time for bed I think." He said smiling at the genius.

"Do I need to remind you that I am not sleeping with you?" The Canadian replied with a nervous confidence. John just rolled his eyes.

"I told you before; I don't want to sleep with you." He said standing and moving to the commissary door. "You coming." Rodney scrabbled out his seat and joined him. They set off down the corridor.

"So where is your room?" John asked suddenly curious.

"Oh it's the nearest one to the lab I could get. It's just the floor above next to the lift."

"Cool." The major said. They walked in silence for a few moments.

"So your last partner…"

"Nancy"

"Yeah, Nancy. Did you two… do you have… what I'm trying to say is…"

"We didn't have kids. We only really started trying just before the disease rendered her infertile. We were 17 we thought we had plenty of time."

"Good… I don't mean good that she was in fertile and died that is, just good you don't have kids. Not that it would be a problem if you did because you obviously didn't bring them with you. Wait that's not what I mean at all." JS stopped and put a hand over the doctor's mouth.

"I get what you mean McKay. You're glad I don't come with a load of extras that you'd have to get used to as well." Having finished he removed his hand from the doctors mouth.

"Exactly!" He said happy that the SO had understood his rambling.

"You do want kids right?" JS asked suddenly

"I don't know. I've never been with anyone long enough to consider it. I suppose passing on ones genes and wisdom to the next generation is a noble pursuit but I've never been inclined to miss that much work, I'm already behind on getting my noble prize by the time I turn thirty." He said waving his hands as though to emphasis his points."

"Noble pursuit?" John snorted. "I just wanna play with the little rug rats. Teach them how to throw a ball or surf." Rodney just stared at him in horror.

"There is no way any child of mine is surfing. Have you any idea how dangerous that is? Not to mention the extent of dangerous bacteria found in sea water." He starred at the SO who was grinning broadly, "Why are you so happy?"

"You just implied that we might be having kids some day." He said smugness evident in his voice, before he walked off leaving the doctor spluttering.

"I made no such implication. This a trial period only."

"You did."

"I did not."

"You so did."

"I did not!" The scientist practically squeaked.

"Deny it all you want but that was a Freudian slip which means you are interested in sleeping with me to have kids."

"I am not."

"See now you're just in denial"

"I am not."

"Are to."

"What are you five?" Rodney complained as they arrived at his room. "Anyway, this is my room so you can go away now." John shook his head,

"Not till I'm sure you're asleep."

"What you don't trust me?" The physicist asked indignantly.

"Nope, you've let yourself have as little sleep as you have. I'm making sure you lie down and stay down for a good twelve hours, even if it means sitting and watching you the whole time." The two men starred at each other for a minute before McKay relented; too tired to argue, the major was right, now he was at his room he really needed to sleep.

"Fine. But you better be quiet." He grumped before opening the door and stalking into his bedroom.

"I knew you'd see things my way McKay." He said following him in closing the door behind them. McKay changed into boxers and a t-shirt in the bathroom as well as brushing his teeth and using the toilet before emerging. John had taken off his jacket and boots before sprawling in a chair next to the bed.

"You're going to need to get a base uniform and go through orientation tomorrow." Rodney commented.

"Yep." The SO said clearly having thought of that all ready.

"Oh, well I suppose I'll just go to bed now then."

"Sounds like a plan." Rodney climbed into bed and closed his eyes before realizing he had left the light on.

"Ummm… Major would you by any chance mind…" The light turned off. Lord the man was quiet.


	2. Chapter 2

**Kajos: Again thank you to cookie62 for correcting all my mistakes**

Rodney grunted and rolled over. He hadn't slept that well in ages he thought as he rubbed a hand through his hair. He blinked lazily around the room and stalled on the bed headed man in his chair. His still sleep-fuzzed brain took a moment to return memories of the previous day. Rodney groaned, he had another SO; he didn't care how smart and good looking he was. Wait, did he just think he was good looking? No he was just some cocky jock. That was all; in a few days the trivial attraction would fade.

He rolled out of bed thumping his feet on to the floor. The SO, John, jerked awake.

"Hey. Sleep well?" The major asked rubbing his eyes.

"Yeah. Like a log actually. I haven't slept that way in forever." John slapped his thighs and stood up.

"Good. What's the plan for today then?" He asked looking for his boots.

"Well first, I think we need to sort out quarters so you don't have to sleep in a chair again. That cannot be good for your back. Then you need to sort your things and go through orientation." Rodney shuffled in to the bathroom to take a shower.

"Oh, and what will you be doing while I'm in orientation?" he called out over the sound of the shower. He didn't hear a reply so he focused on putting on his boots and looking round the room. He heard the bathroom door open and turned to see Rodney with a towel around his waist. He was frozen; the man did not have classic good looks. But his swimmers build and peppering of dark hair hypnotized JS.

"Well, I was intending to work while you're in orientation. Could you pass me a shirt out the drawer there?" He said pointing to the chest of drawers in front of John. He fumbled extracting the clothes and passing them to the other man without looking at him again. He needed to focus.

"So what first? Accommodation, uniforms, or orientation?" John asked as the scientist finished dressing.

"Coffee. First coffee."

"Breakfast, great."

* * *

John stared in wonder as McKay inhaled his coffee from the largest cup he could find in the commissary. "Do you have blood still or is it just caffeine?"

"What's that supposed to mean?" The doctor asked indignantly.

"If you drank more coffee I think you would bounce off the walls."

"It helps me think." He put the coffee down. "Anyway, I'll take this down to the lab you can go do your military thing." JS just stared at him.

"I think you've forgotten McKay. _We _are going to talk to someone about rooms. _Then_ you can go to the lab on the condition that you allow the military to keep an eye on you while I do my _military thing._"

"Look I don't care what you think your roll is here but you do not give me orders." McKay said starting to get annoyed.

"I'm sorry Doctor McKay, I realize your previous SO's might have been lax in their responsibilities but I will know where you are at all times and you will at no time be without some form of military escort. And I am not sleeping in a chair again tonight so at the very least we will be sorting a camp bed being moved to your room for me." McKay grumbled but let it go standing up and staring at the major.

"Well, are you coming?" The man was still finishing his toast. He sighed and stood up; there were some battles not worth fighting. He tossed the remains of his breakfast in the bin and joined the scientist heading to talk to whoever was in charge of room assignment on this base.

* * *

JS grinned at the twin room. It was still nice but a bit more spacious and other than moving McKay's prescription mattress the change of rooms had been painless. McKay had then headed back to his lab while John had suffered through various videos and explanations after signing a non-disclosure agreement. He had then been issued with a heap of uniforms ranging from desert camo to blue and green BDUs for wear around the base. Unlike most of the military he hadn't been assigned to a unit so he wasn't going to get a locker for his off-world stuff. The Colonel suggested that he get an extra foot locker in the room for them and store some of his BDU痴 at Rodney's flat for when they chose not to stay on base.

He smiled at the place that already displayed a selection of both his and the doctor痴 things. He liked the look; he liked the doctor. Far more than he ever expected, he was very quickly becoming very attached to the annoying and frustrating man. Half the time he wanted to tell the Colonel to post him back to McMurdo and he壇 freeze rather than put up with the scientist, the other half he didn't even want to blink in case when he opened his eyes the man was gone.

There was a knock at the door. Major JS turned to see the Colonel.

"I see you were able to get that extra locker." He said with a small smile.

"Yeah, I was expecting it to be harder." JS said with a chuckle.

"Major there is something else I need to talk to you about."

"Great, something other than the fact that we have a wormhole thing that can send us to other planets and ships capable of travelling faster than light?" JO smiled, it was a lot to take in at once.

"Major the gate can do more than travel to other planets, with enough power, it can go to other galaxies. Currently that's what McKay is working on. Providing the power needed for us to connect to another galaxy's gate system. When that happens it will probably only happen once, but this planet isn't big enough for us, we've known it for a long time. We considered setting up on a different planet in this galaxy but with the G弛auld there isn't anywhere safe. The gate we are hoping to connect to is the lost city of Atlantis. We hope that the city will still be intact; we plan to send through an expedition to establish a base there. In the future we hope it will be able to act as an off-world base."

"What does this have to do with me?" The Colonel tool a deep breath.

"McKay's name is down as head scientist for the expedition as our leading expert on ancient technology. That would mean you would be going as well. On a possibly one way trip to a galaxy far far away."

* * *

He was going to have to leave the galaxy, and Rodney had just forgotten to mention this? The galaxy! He stormed into the lab and found it empty except for McKay.

"Where is everyone?" He asked as Rodney finally looked up from his laptop and acknowledged his presence.

"I sent them away, they were giving me a headache," He rubbed his forehead obviously feeling fairly strained and in no state to have an argument with.

"Still got that headache then?" He said sternly.

"Yes, yes, it's just a headache." Rodney said waving a hand to bat away JS's concern,

"They happen often?"

"The headaches?" He asked distractedly. "Once or twice a week." JS's forehead creased in anxiousness. Headaches that bad twice a week was not good, he was clearly overworking.

"Well why don't you take a break and tell me all about Pegasus and Atlantis?"

"Oh yeah, I should have told you about that before shouldn't I?" He says finally pausing in his work.

"Nah, it's not like we're leaving for another galaxy in a month."

"Yes, well I understand if that's a problem, I know that most people have odd attachments to their home galaxies and planets... wait, you said we're. You don't have a problem with leaving?"

"I'm military, I don't have a family really here, my father was military, all his kids went to the forces except my brother, I don't know any of the others and I only met my father when he turned up at the trial over my mess up with Nancy."

"Yes but surely you have friends, people you grew up with."

"No one wanted to know me after Nancy. As an SO to let your partner die is worse than murder." JS said his voice suddenly cold.

"Sorry, I forgot." He murmured suddenly quieted by the other man's obvious disagreement with his question.

"Yeah, well all I have here now is flying and don't get me wrong I love flying. No better feeling in the world. But I'm twenty and I'm alone, and I'm fed up with looking in the mirror in the morning and being ashamed of the fact I'm still alive." He said with a catch in his throat.

"Right, I think this is the point where I should warn you that I'm not good with people or feelings or any of that stuff really, right now for instance all I can think of is; we have no idea what is on the other side. There could be even less for you there." John smiled a little at that, Rodney might be useless with people but it was sweet how he floundered.

"No, McKay because if nothing else I'll be protecting you, that's something. And I'll be giving our world a hope, a new colony on a world of advanced technology? We could have kids, anyone. We could have families. We could live like they used to, free to be what we wanted and to mess up our own lives." He said it so wistfully like he could imagine it and as he said it McKay finally understood why this was important to other people. He had never wanted it to be anything else other than that week where he wanted to be a pianist before the tester told him he was not qualified to be a musician, no passion for it. He had always been expected to have kids, never considered what it must be like to not be allowed to.

"What if it doesn't work out for us though?" Rodney said terrified by the weight of JS's redemption on his shoulders.

"I'll protect you, McKay. Whatever happens that's good enough for me." Rodney just stared.

"No." He blurted out eventually.

"No? No what?"

"Seriously, No. You do not get to just lay that on me, that kind of responsibility for your life." Rodney was getting angry now. "You do not get to make me the entire centre of your continued existence." JS laughed crossing his arms and leaning against the table.

"That's why you got rid of them."

"I have no idea what you're talking about."

"You got rid of your other SO's because you couldn't stand the fact that their life revolved around yours."

"It's not right. I'm you people you follow us around like lost puppies and well I never was a dog person. I like cats, cats tell you what they want and they don't require you to entertain them constantly. I mean, SO's, you never say what you want you just do as you池e told never mind what is important to you. You would spend the rest of your life standing around and protecting me, you would give up any hope of actual happiness for what? Duty, that's the big stickler, you know, duty."

"Rodney, we have our own minds, I've thought about this." Rodney scoffed at the reply.

"You've be raised to protect me, you've been conditioned that this is what you should do. You have no choice in the matter it's your primary purpose. It's programmed into you. That's not a choice."

"Rodney, if I don't go with you I'll be standard military for the rest of my days. Any way SO is just a title without the job. I can do that in Atlantis as well as here and keep an eye on you as well." Rodney continued to stare him down.

"Fine, so you want me to make a choice but any choice I make is invalidated by who I am." Rodney waggled his head from side to side.

"Well...yes. I suppose you could put it like that." Sheppard rolled his eyes.

"WHAT DO YOU WANT FROM ME!" Sheppard shouted slowly at him.

"I don't know! Okay? I hate this, this whole thing is messed up. I mean come on, the population is already significantly lower than it used to be and current population trends mean that if we ceased sterilization and simply restricted people to sustainable family sizes we would have centuries before population growth became problematic again." Sheppard starred at him in shock.

"YOU'RE A..." Sheppard stopped and dropped his voice. "you're a disbander?" he whispered.

"I'm Canadian. I work with the Stargate program for the betterment of the earth as a whole. That doesn't mean that I have to believe in what you池e doing, or your approach to the military." The scientist hissed.

Two decades previously the Canadian government had decided to change policy, since the early 20th Century they had spent 70 years enforcing the breeding program along with the western world, but just before his and McKay's birth they had decided that the scheme was no longer necessary. They had returned to a more classic family model. Children were still trained from birth for a profession but they were not separated for their parents and the military had been reintegrated into society.

"So you weren't taught about SO's."

"The American government required me to accept an SO as a part of my contract... to protect their interests. They also required me to agree that my first and third child would be subject to the normal requirements of your country."

"And you agreed to that?" Sheppard queried on the basis that he didn't seem to agree with American military policy at all.

"With certain conditions, I don't want them to be alone, I want to be able to contact them, spend time with them and know them." He said desperately "My parents were both raised separated from their parents, they were civil servants. They were terrible parents; they blamed me for all the problems in their relationship. They didn't want the responsibilities of raising a child; they both felt that as someone of high intelligence I should be the responsibility of the government. No child deserves that, to be fobbed off on a government organization because no one else cares about them." Sheppard felt his heart break for the man who had been so unwanted. Sure he had been raised in a dormitory but he had always felt appreciated and wanted by his superior officers. He had always felt that he was important because he would be needed to protect the civilians of the USA.

"Rodney, this is hard for me. I've always been taught that Canadian policy was crazy and wrong, mostly because your country risks leaving people like you unprotected."

"John, we're not the only ones. Scotland, the Channel Islands and New Zealand have followed in revoking the policy. Look, just leave. I don't need you here and you won't want to be here soon enough. Surprising as it may seem, most people don't really like me." Rodney looked deflated and lost as he turned back to his work. John grabbed his arm.

"I'm not leaving. As I said, I may not agree with all that, but you池e right about one thing. No one deserves to think that no one cares about them, to be left in the care of a government because no one wants them. That includes you. You deserve someone to stand by you. Someone to give a damn about what happens to you beyond your ability to work and produce results." Sheppard starred at him until he looked him in the eyes. "That enough of an independent decision for you?" McKay looked at the Major痴 determined face and the genuine concern in his eyes for the fact that McKay thought so little of himself and his emotional needs.

"Yeah. It's enough." He said with a small nod.

"Good. Now, let痴 head to the infirmary and get someone to have a look at that head. I don't like the idea of you having persistent headaches."

"Oh, my god, are you always this naggy?" He whined.

"Yep." JS said simply.

**Kajos: I think I like that as a place to end this chapter. Hope everyone is still enjoying it.**


	3. Chapter 3

Kajos: Hey readers I'm sorry this update has taken me so long but I hope you enjoy it. I'm dedicating this one to the memories of all those who have been sent to war and lost something because they were following orders. To all the lions led by donkeys. And again thanks to Cookie62 for being so much better than spell check.

* * *

JS finished up in the gym and left in search of his genius. As he headed for the lift he spotted someone with supplies marked with the Atlantis expedition logo and it hit him. They were leaving in a week. After three weeks of intense training by the staff of the SGC, as well as a lot of intense shouting by McKay whenever Sheppard told him no and dragged him away from his work, McKay was finished with the calculations and was now busy organizing his team and equipment for the possible one way trip.

JS arrived at the lab to find just McKay and Zelenka there the minions having been sent away. Zelenka was a constant source of confusion for JS. He was clearly a genius but every IQ test said he was just outside the bracket for requiring an SO. JS still couldn't decide whether he was just that smart, but modest as to cheat the test, or if his intelligence was something outside that of an IQ test. Either way McKay constantly ranted at him and the Czech would simply ignore the man making JS smile, the two scientists were the perfect contemporaries.

"Rodney." He said standing in the doorway.

"Yes, what is it now?" Rodney's resistance to his presence and yet insistence that he refer to him by his first name was another puzzle JS was still working on. The mountain seemed to be filled with them as well as a lot of people with controversial view points.

"Food." He said simply.

"I've already had lunch I'll have you know."

"Yes and now it's seven in the evening and time for dinner." the Major said with a smug smile. Rodney looked at his watch before grumping about him being right. Thankfully Rodney didn't resist that much to being fed; it was sleep and not working that he and his SO were constantly coming to blows about.

"Fine but we're going to get real food, I feel like steak."

"I think they're only serving meatloaf."

"I meant real steak. There a place called O'Malley's in town, we can go there." Rodney said as he closed down his computer and pulled his jacket on. When he turned back he saw that John was looking uncomfortable.

"What wrong with you?"

"Nothing it's just been a while since I ate out." Rodney just sorted and headed past him towards the lifts. "We better stop off and change. I can't take you there dressed in those." John was wearing his navy blue SGC SO uniform. He joined Rodney in the lift saying nothing as they headed to their shared room. On arrival Rodney switched his Atlantis expedition jacket for a civilian one before turning to look at John who was stood just inside the door looking lost.

"I don't have anything except uniforms." He had had only ever had a suit and a pair of jeans when Nancy was around for when she wanted to go out. He had gotten rid of them when he moved to Antarctica as unnecessary.

"Seriously?" The genius asked. All his other SO's had at least had a set of civilian clothing. John just shrugged. "Fine." Rodney huffed pushing past him towards his clothes. He rifled through the various iterations of navy, khaki, olive green and black. Finally he found a simple pair of black trousers. Which he threw at the SO, followed by a black Tee. "Keep the trainers on." He said indicating to the white trainers John was still wearing from his trip to the gym. Not uniform but allowed for off-duty as exercise shoes. After that Rodney abandoned Johns clothing leaving it looking as though a tornado had hit and moved to his own clothing. He shifted through everything he owned. Oddly his clothes didn't appear to get any messier than they were in the first place. Finally he turned to see the SO standing straight in the trainers, straight edged black trousers and tucked in T-shirt still looking every inch the member of the military that he was. Rodney simply threw a shirt of his at him. While it was allowed for SO's to wear civilian clothing when with their geniuses in order to avoid drawing attention John had never felt comfortable about it. He pulled in the large white shirt and rolled the sleeves up to his elbows to hide the fact that they were a bit short on him. Then he did up the shirt half way. He would have continued but Rodney had glared and he had left it. Rodney starred at him a little longer then nodded and handed him his large winter coat that just about fit him.

"We're going to have to go shopping tomorrow." He said as they headed back to the lift. John didn't say anything. He hated going out into the civilian world. There would be so many people everywhere to keep track of. That and he felt out of place, like a fish out of water.

* * *

The restaurant car park was busy as John parked the jeep, Rodney's directions had meant the journey took them well over an hour as Rodney shouted at him for missing turnings. JS was instantly on guard when he noticed a few people leaving intoxicated.

"I thought you said this was a restaurant."

"It has a bar as well." JS didn't like this one bit. Nancy had always been shy, small cafés and things, they had left when they were so young he had never had to go into one of these places let alone had to look after his SO in one. Rodney noticed his reluctance.

"Oh, come on I know you're military but even you lot have bars." That might be true but JS had never been in one.

"By the time I was 18 I was shipped off to the great south, not many bars down there and then I haven't had a reason to think of going in the last three weeks."

"18?" Rodney asked "I thought the legal age here was 21."

"That's for civilians Dr McKay. Military age is 18, never known why but that's how it is."

"So how old are you?" Rodney asked suddenly realizing he didn't know.

"20" Rodney was surprised the man was actually two years younger than him.

"Anyway, let's head inside. I'm freezing out here." He said heading for the door so John trailed along behind him until they actually reached the entrance when he placed a hand on the other man's shoulder so he could enter first just in case. Rodney rolled his eyes but acquiesced. He had had enough SO's to know that when uncomfortable they got very protective and if he pushed it at that moment he'd probably have been thrown over a shoulder and carried back to safety.

* * *

McKay was a bit of a regular at the steak house, he went there every time he got fed up with the mountains meager fair. He was recognized instantly.

"Ah! Dr McKay, it's been to long since we last saw you. I'll make sure your waiter and the kitchen staff are reminded of your dietary problems." the host said pre-empting the scientist. Rodney instead held out a hand towards John.

"Table for two this time." The host smiled at him.

"We're a little busy right now but if you and Mr..."

"Major JS." John filled in.

"Ah, I'm afraid Dr McKay we are not licensed to serve the military." He said quietly obviously thinking something untoward was going on. JS pushed in front of his genius pulling out his dog tags including a extra tag that marked him as an SO and contained on one side were Rodney's details. O'Neill had given him the tag the day after he arrived.

"A license won't be necessary." The man's eyes widened a little. Though military would never be served in a civilian bar he considered it an honor to have an SO in his establishment. It meant that Dr McKay was a genius and those were something to write home about. It also meant that the SO thought the place safe enough for him to venture into which given the doctor's allergies was a great compliment to his business.

"W...Well if you wait a moment in the bar I'm sure I'll be able to find you a table." He said making a not to himself to inform the staff that not only McKay was in the building so to hide all the lemon but that he had a possibly homicidal body guard so hide it well.

John surveyed the bar and selected a seat for him and Rodney that was easily defensible.

"What do you want to drink?" He asked McKay.

"Did you have to pull those out? They make you look like a dog with my name and address on your collar."

"What do you want to drink?" He asked again ignoring the comment.

"Beer." was the simple answer this time. As JS turned to the bar he saw the host mention something to the barman who glanced their way before suddenly rushing into action. John heard complaints as suddenly slices of lemon were yanked out of drinks and thrown away as he approached. The SO smiled a little he missed interacting with civilians like this in a way.

"Can I have a Beer and a Pepsi?" He asked at stressed man behind the bar.

"Yes!" He said instantly and grabbed a glass and started pulling beer off the tap. "Um...What's Pepsi?" He asked JS suddenly. That threw the SO who had been scanning the room for threats.

"It's...brown, fizzy, sweet soda with caffeine?" The Barman starred for a second.

"Coke?" JS just shrugged and the bar man pointed to someone drinking coke.

"That looks like it." The civilian nodded and grabbed a bottle and a glass before handing that and the beer over to JS. Who tried to hand him back some money.

"No charge." JS just nodded and took the drinks shoving the money back in his pocket and returned to his charge.

"That took forever." Rodney commented on his return.

"Hey, it's not my fault the guy doesn't know what Pepsi is."

"You should have asked for Coke." The Doctor said having been around military enough to be aware that while civilians drank Coke the military shops and such stocked the slightly different Pepsi drink. While Rodney started in on his beer John sniffed the mysterious Coke stuff and gave it a sip, it tasted odd.

"So what happened to the people you grew up with? They just abandon you." Rodney asked before wincing at what he realized was an extremely insensitive question.

"The rest of my litter went into the normal forces; I kept in touch with them as I still did a lot of standard training with them. They were infantry. I became a pilot as the nearest SO section was the airbase down the road but in many ways I was still close with them. Then there was the conflict with Mexico when they moved for independence. Everyone knew it was stupid; it wasn't soldiers they weren't fighting. They were ordered to march on the rioters over the border and regain control. They were 17, facing civilians armed with whatever they could find. They had guns. They marched in there and were slaughtered without a shot being fired. I mean the primary duty of a soldier is to protect the civilians, they knew that the civilians knew that, but they were still ordered to march into that riot." Rodney didn't say anything. He couldn't imagine losing his sister. Sure they hadn't talked in years but that didn't matter and yet John's entire unit had been slaughtered. His litter and most likely those that raised them would have all been gone in one day.

"Sometimes following orders is the wrong thing to do."

"Yeah but they weren't SO's, they weren't even officer yet. They were three months off from being trained to assess situations. It was assumed they wouldn't need it that young."

"Well that was wrong wasn't it?" Rodney was really kicking himself here. Him and his big mouth, he was just making this whole thing worse. John nodded a little.

"They changed protocol after that when none of them turned around, training's now at 15 instead of 17." _F__at load of use that is to you._ Rodney thought.

They were silent then until the host returned to say their table was free. Even then their talk was mostly about what they were selecting and John insisting he try all of Rodney's food first to make completely sure there was no lemon in it. That made Rodney smile as the man plucked bits of food off his plate and offered them to John, in the past all his SO's had interrogated the staff of places they ate out but none had ever just tried his food. He liked it.

"We need to talk about where this is going." John suddenly said when they were half way through their main course.

"What! Why?" Rodney spluttered barely managing to swallow before he accidentally spewed food on everyone else.

"Because Rodney, currently I'm only on temporary assignment to you. Is this going to be permanent? 'Cause if you're benching me then I need to know, otherwise you won't have an SO next week when you leave. I need to know if we are likely to be having sex and kids at some point so I can pack stuff like lube and stuff for us and things like baseball gloves and stuff for kids. I need to know if I need to make sure there are enough kid's clothes and things in case we want to have kids."

"You can't expect me to be able to answer all that! I've known you all of three weeks!" Rodney was in shock that his mostly quiet SO had just come out and asked him if they were ever going to have sex.

"Rodney, calm down. I'm not asking to marry me and have sex and kids right now. I don't want that right now but I know that in a few more weeks or, months I'll be ready to sleep with you and I know that I'll want kids when we're ready for them. That's me though. I need to know if you're ever going to be interested in those things."

"What happened to staying with me no matter what?" Rodney cried not having listened to the start of John's statement.

"That's still there. If you told me right now that you want me to remain your permanent SO but that we we're never going to have sex then I would be fine with that, but I need to know."

"Can...Well...I'll need you to...Just let me think about this John, okay? I don't... It's a lot of stuff you're asking that I haven't really thought about yet."

"Okay." Was the military man's simple answer and they waited for their deserts in silence.

Kajos: Sorry it's a short one, I don't own Pepsi or Coke. By the way for those who can't tell I am British and I apologize for when I forget to use Americanisms but I dislike torturing the English language. I'll do my best with speech but narration will almost always be in proper Queen's English.


	4. Chapter 4

**Kajos: Yes I'm finally writing the next chapter, sorry it's taken forever please see the apology on my profile as to why.**

Rodney wandered around the mall while JS trailed after him aware but uncomfortable. He had thought the physicist was joking about the clothes shopping but he had been deadly serious. It also seemed that a couple of cheap pairs of jeans and a shirt weren't going to be enough to keep Rodney happy.

"_Look, John, I'm not going to have you trailing after me looking like you just fell into a charity bin."_

Had been Rodney's reply when John had suggested as much. So far Rodney had insisted on three pairs of jeans, four t-shirts, two shirts, a pair of slacks, a suit jacket and a leather jacket. And apparently they weren't done. Rodney dragged them into yet another clothes shop. John wasn't even paying attention anymore.

"Here" said Rodney shoving something into John's left hand, he knew better than to fill the SO's right hand. John looked down at the article and handed it back.

"I do not need a robe." He said.

"What? It's a staple piece of clothing."

"Rodney, I only need clothes for going out with you. So unless you're into something your not telling me about. I don't need a robe."

"But, why won't you want one. It's far more comfortable than those scratchy towels you insist on wearing when you come out the shower, and we don't know what the place we're going to is like, it might be freezing then you'll wish you'd taken the warm fluffy robe."

"Well if it's cold I'm sure I can think of something I can do to warm up." He said meaningfully. Rodney spluttered at the man's sudden change in tactics. "I don't need anything else, so I think it's time we stop for lunch," he said checking his watch and noting the time since Rodney's last meal, "and then head back so we can talk about packing."

"I want you to come." Rodney blurted at him, realising he hadn't made that entirely clear the night before. "I want you to be my permanent SO. Your too good at the job to get rid of. I mean you remember food with out being bossy, you always check for lemon without being overbearing, and you actually get me to sleep with out completely pissing me off, and oh my god that made me sound like a child!" Rodney exclaimed the last part having realised what he sounded like.

"No, it makes you sound like a genius who's to busy saving the world to be thinking about silly things like that, which is what I'm here for." Rodney raised an eyebrow at John's smooth answer.

"I thought you were here to keep me safe and fuck me." He said his mouth twisting at the sides.

"I'm working on it, genius, just give me time." John said once again checking his watch as he guided the scientist out of the shop and towards the nearest cafe.

* * *

When they got back to the room JS grabbed a pen and paper and started writing a list of what he would need to pack. Between then they would be able to take one crate of personal items plus a bag each. John put down clothing and toiletries for both of them, then he started putting down all the other things Rodney would need, pictures, chocolate, movies, music, books and TV series that John planned to have put on a hardrive for him. By the time Rodney wandered other to look at the list he had pretty much filled the crates and was about to start on the bags, by his reckoning.

"Hey, that's all my stuff."

"Yeah. What else would go in there?"

"I don't know maybe your stuff?"

"I put my clothes and soap and stuff down."

"What about other things? Don't you want stuff like a picture of Nancy? Or your kennel? Or anything personal?"

"I don't have stuff like that. There never was a picture taken of my kennel all together. There was no reason for it. I had a picture of Nancy but they confiscated it when she died used it in the tribunal then through it away. I don't need pictures and things."

"John, seriously, I want you to have things like that. I creeps me out that you have so few attachments, that your entire life comes down to clothes and soap."

"And you." John said softly. "All this stuff it's you, I want to see you every where when I look around the room. Your so alive and vibrant and real."

"Fine, but make sure you take your civilian clothes as well as your uniform."

"Why?"

"Because every now and then I'm going to want to hang out with you as though your not a major. Like your just some guy." John looked up as Rodney put his hand on his cheek.

"Okay, what about the other stuff we talked about yesterday? Do I need to pack for that and make the expedition supplies aware?" Rodney swallowed looking down at his hopeful and beautiful face.

"Yeah, I'm still not ready, but yeah. You better tell them." John's face lit up like the sun and Rodney couldn't help smiling as well.

* * *

They would be heading up the ramp any second now. John starred in wonder as the ring span he had seen it before but today it was a mark of the reality, he was going to a world far away that he probably wouldn't be coming back from any time soon to colonise with this group of people including the smartest man in the world. His Genius.

"Well, are we going?" Rodney snarked at him.

"Of course Dr McKay. As soon as you stand behind me and promise not to move more than a metre from my side once we're through."

"Of course of course." The man said shuffling back down the ramp to stand behind his SO and push him forward towards all the shiny new technology just waiting for McKay.

**Kajos: Sorry it was short but that's the end of part one of the story and I'll be starting on part two today.**


	5. Chapter 5

Rodney was pissed, and everyone knew it. He was shouting and ranting and throwing things. JS had had to be heavy handed with him for days now to get him to sleep and eat and such. He wasn't talking to JS though because the other thing everyone knew was why Rodney was pissed. JS was why. On arriving in Atlantis they had discovered that most people couldn't get anything to work. Beckett had suggested a theory of his that it had to do with having a certain gene. It turned out Rodney didn't have it, but John did. By the bucket load.

So Rodney was pissed because his SO had won the gentic lottery and he hadn't and had to get one of the list of gene carriers to activate everything while they worked out how to make the place more accessible.

"Look, Rodney, if I could give you my gene I would. I can't though so why don't you look at it as having one up on the rest of the scientists who have to book time on a rota to get access to a gene carrier where as you have one standing next to you the whole time."

"It's just ridiculous. What possible purpose could you have for the gene, where as me? I'd be the perfect person for it." Rodney complained when JS finally gave in and locked him in their room until he talked.

"Are at least done with the pettiness. I miss actually having conversations with you, and though I love you I'm fed up with having put you to bed all the time." JS said his eyes a little sad when he looked over at the bed Rodney slept on and the near by camp bed he used. He had no problem with it as a place to sleep he had spent a large amount of his life on similar beds but he wished he could share with his genius who he knew was a cuddler from the way he hugged his pillow. "Now, lets go get breakfast."

"But it's that weird stuff they brought back from the planet."

"Look, have breakfast with me and I'll take you exploring this afternoon." He promise coaxingly.

"Are you trying to bribe me to have breakfast?" John grinned at him.

"Is it working?" Rodney smiled back at him.

"It might be." JS placed a hand on the small of his back as he lead him out the room the door opening in front of them with his gene.

In the initial determination to find quarters and food after the city rose out of the water not much had been explored at all. JS had got permission early on to escort Rodney to explore these areas as it gave them a chance to spend time together which had been sparse since arriving on Atlantis. They wandered into a large room with tiers and pods on the walls. JS's eyes lit up at the site he knew instantly what they were knew it in his bones as they seemed to call to him. This is what he was born for. For the first time ever he was deaf to what ever it was Rodney was saying. If someone had attacked Rodney in that moment JS would have ignored it as he walked towards the pod sat in front of him.

He opened it and stepped inside watching it light up around his as he headed for the chair at the front. He sank into the seat and ran a loving hand over the controls feeling it leap into life like an eager dog. It wanted to be flown and it wanted to be flown by JS, no, it wanted to be flown by John. He gripped the steering in his hands and was about to take off when the pod alerted him. It seemed to be able to read his mind. It refused to start engines and John got a sense of disaproval. He looked to his left and finally listened to what Rodney was saying.

"this thing is ancient, it's been sat around here for thousands of years. Who knows what systems might be damaged and if something like the inertial dampers were to fail mid flight we'd suddenly be dealing with killer g force." He couldn't fly it with Rodney there. It was too dangerous and some how the pod had known that, even when John was blind to his duty the pod had seen it and refused to let John do something he might later regret that much.

"Okay, Rodney, I was just looking."

"What was with you then? It was like you weren't listening to a word I was saying."

"I'm sorry but there was something about this thing. I couldn't help my self. It was like I had to sit here."

"Wait are you telling me that ancient technology is pulling you in?" John wobbeled his head in thought for a second before nodding. "Right, we're out of here right now. Out out out out out." He said shooing the Major out of the pod.

"Whoa, hold up, Rodney whats wrong?"

"What's wrong? It's pulling you in! That suggests it has a level of influence on you thanks to you gene that I'm not comfortable with. I mean what if this thing goes both ways and not only can you control their technology but it can control you? Think about it." Rodney said still dragging John away from the pod.

"Rodney, we can't just leave these things, they're space ships that can go through the gate." John pleaded.

"I know gatehsips, very cool, very dangerous to you. We're leaving I'll send Zalenka down later to check it out and if, note if, he clears them as being safe I might consider letting you back down here. In the mean time we are going to talk to Beckett and then see if Elizabeth has done any translations that might mention this pull." Rodney said as they went back to the transport/lift thing they had found early on.

It had been a busy few days to start with, they had been trading with a people on another planet for food and heard stories about fearsome wraith who sounded a lot like vampires. John was cynical about it but apparently they're trading partners were adamant they existed. So JS was on high alert when he and Rodney went through the gate to their planet. Rodney had heard that they had a ruined ancient city there and wanted to check it out so after days of begging JS had agreed to it.

When they got there they were introduced to Teyla the peoples leader, who agreed to show them the old city. It was some walk and JS kept pointing out that it would be so much easier in one of the puddlejumpers as he had taken to calling them. It was catching on though Rodney still insisted on calling it a gateship.

"Here is the city." Teyla said as they rounded some trees and it came into sight.

"Looks like a ruin, Rodney." JS said picking up a trinket off the ground.

"There still might be something hidden, we've seen it before back in the Milky Way." Rodney pointed out.

"What's that you have there Major?" Teyla asked.

"Oh, just something from the ground." He said showing it to her.

"It is a necklace of mine, my grandmother gave it to me I lost it as a child. I thank you for it;s return."

"No thanks needed, Teyla." He felt uncomfortable with using her first name.

"If it will make you more comfortable Major, you may call me by my last name, Emagen."

"Thank you Miss Emagen. I would prefer it."

"I find you culture fascinating in it's customs." She admitted, "Among my people we have no division between warriors and others as you do."

"Not every where does. Where I come from there they don't have the divide they do in John's country. I find though that trying to convince John of the lack of need for it is a futile pursuit." He said as John glared at him.

"Look Rodney, there's nothing here we're going to find in the next three hours. Lets go back and you can look at more of those translations and then maybe you can finally get other the paranoia and let me back in the puddlejumper."

"Oh, get over the puddlejumper!" Rodney said.

"Quiet, I sense the wraith."

"You can sense them?" JS asked.

"Yes it is a gift in my family. We must get back to the village and warn them."

"But the others, the colonel are all back in the village." Rodney babbled.

"Yes, which is why we must return to warn them." Teyla said gently as JS grabbed Rodney and they all started to run for the village.

"Sir, Teyla has told us that the wraith are coming."

_"How can she tell?"_

"She says she can sense them."

_"Right, sure." _Came the reply over the radio sounding very uncertain.

"Look, we're coming back to the village we'll be there soon, you can talk to her yourself." He said before ignoring his radio and focusing on running and pulling Rodney along with him. Teyla was glancing up constantly in fear. It made JS more and more nervous as they ran they were a good twenty minutes from the village at a run. There just wasn't time before they heard it.

The whine, the swoosh of the beams. The wraith were taking people Teyla told them. Everyone was making for the gate. The Colonel was evacuating through the gate to Atlantis. JS could think of nothing but running faster, getting to the get sooner and avoiding any of the ships they had seen coming overhead. He could hear one approaching and quickly dragged Rodney forward starin over his shoulder watching the beam coming. It wascoming strainght for them. He threw his weight into the genius moving both of them out of the way at the last second and as they fell JS looked forward in horror as Teyla disappeared into the light. As soon as it was gone though JS was back on his feet dragging them both towards the gate.

JS barely remembered what had happened as he hovered over his genius he had insisted the moment they were through the gate on getting Beckett to check him for injuries. He was there when the young Lieutenant entered.

"Major."

"What is in Lieutenant?"

"Well, sir, we lost the Colonel on the Planet, that makes you the ranking officer."

"What?"

"We await your orders as pertain to the current situation and Dr Weir would like you in the conference room to discuse the viability of a rescue, apparently one of the boys we brought back with us from the village has an address for where the Colonel and the others will have been taken."

"Rodney, might be hurt." JS said as though that answered all the issues raised.

"I'm fine John." Rodney said hopping off the bed. "Let's go." He said grabbing his jacket.

"I don't know what you all expect me to do. I'm an SO not a commanding officer."

"I'm afraid you are now sir." JS was lost but Rodney grabbed his arm and started to drag him out of the room following the Lieutenant towards the conference room.

"Major, good to see the Lieutenant was able to find you. I'm sure you are aware we have several people missing and that we may have a lead on their location." JS just stared at Doctor Weir not entirely sure what to do. Rodney watched him flounder for a minute before grabbing his sleeve and pulling him out the room.

"Give us a minute," he told the civilian commander of the expedition. Once the doors closed behind them and they had the corridor to themselves Rodney turned to John. "John, you need to focus, you can do this. If you can keep me up to date on my sleeping and eating and not drive me into a rage every five seconds, you can do this."

"I have no idea what they want from me, I was never trained for this."

"Newsflash John, I wasn't trained to repair and maintain an ancient city, I'm doing it anyway. Elizabeth wasn't trained in running a colony of military and civilians from all over the world. She's doing it anyway. None of us were trained for this, John. But John you can do this. You can step up to this and be a great leader for these men. Now get back in that room look at the options the same way you look at my menu choices when we eat out and make the best pick, just like always. " Rodney's bizarre pep talk seemed to have knocked John back into his sense and he nodded.

"Right Dr Weir, from what I can see if we go after our people we have no idea what we are going into. We can't afford the protection of numbers so we'll have to take a small group and hit them quickly and quietly, hopefully we'll be able to get in and et out with the captives before they know we're there. I want to speak with the Athosians, I need to know as much as possible about what to expect. Lieutenant I want you to put together a team of eight people, we'll need Special Forces, anyone with surveillance or demolitions experience as well. Rodney, I'm going to need a gateship, I know your not happy with them yet but you said it and a cloak and that might be the advantage we need to get through the gate and back unnoticed, plus it will mean the wraith won't be able see which co-ordinate we dial. I will, take the next hour to talk with the Athosians and then I want the team together in the gateship bay and a jumper ready to go. Is that all okay with you Dr Weir?"

"Sounds like a plan Major. I wish you the best of luck you have everyone's support. "

"Thank you, where will I be able to find the Athosians?"

"I believe that we currently have them housed in the cantine." John nodded and turned back to Rodney for the second time. "Rodney, I'm going to be busy for a while, I need you to promise me that you will sort the gateship and then have something to eat and go to get yourself checked out in the infirmary. Then go get yourself some sleep." Rodney opened his mouth to argue. "No Rodney, don't argue. I need you to do this, I need to know that you are going to be okay, so that I can focus on getting those people back here and safe." Rodney swallowed and nodded. With everything sorted John took a deep breath and headed for the cantine.


	6. Chapter 6

**Kajos: I apologise for the long time between updates. I have the rest of the summer reasonably free though so I should be able to update more often.**

Rodney was sat in bed with his laptop when John finally got back.

"Hey." He said in a tired voice as he entered/

"Oh, hi. I know you said to get some sleep but I couldn't so I thought I'd do some work." John staggered over to his bed and vegan to strip.

"Don't worry about it. I… just don't worry about it." John said refusing to look at Rodney who closed to laptop and pushed it under the bed.

"Okay, what's up, John?"

"Nothing, I'm just tired."

"John, there's something wrong. Just tell me."

"It's not important Rodney. Just go to sleep."

"John, you're not acting like yourself. This is clearly important to you, which means it's important to me. What happened?"

"I killed MS, is that what you want to hear? He was kneeling and helpless and I killed him!" Rodney sat frozen for a moment after John's out burst. The he stood up and approached John from behind wrapping his arms around his waist and resting his head on his back.

"What happened?" He asked quietly. John sobbed unable to completely contain himself any longer.

" That thing was killing him, ageing him. He looked like he was a hundred. He saw me and his eyes… his eyes asked me to end it. So I pulled the trigger and put a bullet in his brain."

"Oh, god." Rodney had to breath for a second. "You did the right thing."

"I killed my commanding officer."

"He was dieing in a slow and painful; manner you couldn't stop."

"I could have thought of something."

"John, please don't do this. Your tired, lets get some sleep."

John nodded and stepped out of Rodney's arms to turn down his bed only to have Rodney take hold of his arm and pull him back towards his bed.

"Rodney, don't." John said in a pained voice.

"Why?"

"I don't want it like this. I want it when your ready, not when you feel you aught to."

"John, I _want_ to comfort you. I _want_ you with me tonight. I was sat here awake with worry at what would happen to you. I _want_ to hold you tonight and know your okay." John stared at the open concern on Rodney's face and acquiesced. They lay in bed with John nearer to the room and door with Rodney lying half over his left side leaving his right hand free to reach for the gun on the nightstand. John fell into a peaceful sleep, dreamless and without nightmares of the rescue mission. It was wonderful and John loved Rodney for saving him from himself that night. The next day John would have to decided what to do as the new commander of Atlantis's military and Rodney's SO, particularly with the new threat of the wraith that according to the one he killed would only get worse from now on. But that would all wait till the morning, that night was for the two young men, only just adults to enjoy and be together.

* * *

The next morning, John woke to a warm weight on top of him and a loud knocking at the door. Opening his eyes he carefully pulled himself out from under Rodney and went for the door. Outside was stood Lieutenant AF.

"Good Morning sir. I tried reaching on your earpiece but you didn't respond. Dr Weir has requested a debriefing in an hour and there are various rota's and paperwork for you to take care of in your office."

"Wait." JS said holding up his hand. He looked behind him surveying the room before stepping outside and closing the door behind him. "First, Lieutenant, you are never to wake me knocking on this door outside of office hours. I will not have you waking Dr McKay with these issues. Second, what office? I can't sit in an office all day. I need to be in the labs with Rodney."

"Sir, you are now commanding officer of this base, you'll need to do the paperwork some where. I guess you could talk to Dr McKay about a desk in the lab but I'm not sure that would be appropriate as you will also need the space for confidential paperwork, and addressing issues with the men."

"Fine, where is MS…my office?"

"It's in the corridor leading away from the gate room."

"No, that won't work. That's minutes away from the labs."

"John! John!" Came the shouting from inside. John ignored the Lieutenant and went back into the room.

"Hey, hey, Rodney, it's fine I'm here." John said rushing to sit on the bed and run a hand through Rodney's hair.

"I woke up and you weren't here and the light's weren't on in the bathroom."

"It's okay, I was just outside talking to Lieutenant AF. I never left."

"I thought last night might be a dream and you hadn't come back." John hushed him pulling him close while Rodney calmed himself.

"Right, I need to go back and talk more to the Lieutenant, I'll be just outside, that okay?" John asked a few minutes later.

"Yeah, that, that's okay." Rodney mumbles catching his breath. John let go and slid away from Rodney before smiling at the scientist and going back out the door.

"Sir, this is important business. I think it should take priority over Dr McKay's nightmares."

"Lieutenant, have you ever worked with an SO before?"

"Not directly, sir."

"Well, let me explain something to you. Rodney's well being always comes first so unless it's some one in peril, or in danger I will deal with Rodney first."

"Sir, the well being of one man can not be placed above the running of the entire base."

"I am an SO, Lieutenant. That mean's my job is to look after one Rodney McKay. Get used to the fact that SOs put their Geniuses first. If you want to contact me in future if you need to get hold of me, email. I promise I will check it first thing in the morning, so unless someone is dieing, don't knock. I'll be at the briefing, get me a list of rooms closer to the lab that I could use as an office and for god sake read up on dealing with SOs before you piss me off anymore." He said before storming back into his room.

Rodney was sat pulling his shoes on when he entered.

"Hey, John. Look I'm sorry about earlier, I don't know what came over me."

"No that's fine. Rodney, you are welcome to ask me to be there for you when ever. Now I have a debrief in," John checked his watch picking it up off the side table "40 minutes. So we need to get dressed, have breakfast and get you to the lab. I'll be back after the debrief to talk to you about my office."

"Wait, slow down, office? Since when did you have an office?"

"With… with the Colonel gone, I'm now the head of the military. So I apparently have a lot of paper work and… and meeting with members of the military and stuff, so I need an office."

"I didn't think about that. So you're now the military leader. What does that mean for us?" John froze holding his boots.

"Nothing, Rodney, it changes nothing for us. I'm still here for you, we're just going to have to be creative about how we make sure you feel safe and my protective urges are satisfied in all this, but we'll work something out."

"You don't have to John. Look you have a bigger responsibility now. That's okay. I'll check the room assignment and see if I can find you a new place."

"Don't you dare, Rodney, I need you to do this. It wouldn't matter if I moved out and handed responsibility over to someone else, I will not be able to do my job unless I'm sure your okay. I am your SO, that's who I am now Rodney. So I need you to back me up on this, I need you to be there for me." Rodney swallowed at the need in John's voice.

"Okay John. Now, we're dressed I think the next thing on the list was Breakfast so lets go."

* * *

John stared around the empty office space, it was two rooms away from the main lab where Rodney worked. It was good. He could get a desk in there and a laptop and have room for a couch as well so Rodney could crash in here if he needed to. He needed something though, it was closer to the lab but he still didn't like the idea of being sat there not able to see or hear Rodney, anything could be happening to him.

"Lieutenant." He said calling the man over from where he was stood near the door. "I want you to move a desk, the files, two chairs and a couch into here. I'll be back in a bit. Once I have this all set up I will look through all the personnel files and then sort out rotas and stuff. I mean I can't do one job properly with out doing the other first."

"Yes sir." The Lieutenant had stopped questioning his superior officer earlier, he had spoken to some other people and they had all said the same thing, he was being stupid about the CO being an SO. That was how SOs worked and AF should get used to it sooner rather than later. The Major left then, AF watched him walk along the corridor to the main lab.

"Rodney, can we talk?"

"Sure…sure… sure. Just let me." He hit a key on his laptop and then spun on the chair to face John. "Okay, I'm all yours."

"Rodney, could we put some camera's up in here?"

"Camera's? Why?"

"Because, I'm going to have to spend most of my time in my office and not here and I can't see or hear what's happening with you while I'm there. If we put up some camera's then we could link it to my laptop in my office and I could keep an eye on you and get my work done."

"You want to put in nanny cams so that you can watch me while you work?"

"Well, yeah. Not that I don't trust you, just that anything could blow up or attack you and I wouldn't know. This way, I won't have to worry."

"You know that is way cuter than it should be."

"So, it's okay? You can set it up." Rodney sighed and looked around at the lab full of jobs that needed doing, then back at John's face.

"Yeah, I can set it up. I'll have it done by the end of today. But only in the lab, okay."

"That's great Rodney." John said stroking the side of his face. "I'm going to go get a sandwich for each of us, then I'll come back and sit and read personnel files in here while I wait for my office to be sorted."

* * *

Rodney also seemed to move into John's office. With in the first month there was a second desk in his office and a white board full of scribbles and equations. The physicist had taken to using the office as a place to do work away from his lackeys. John liked it. It meant he got to do his work while getting alone time with Rodney. They grew closer sitting next to each other on the couch with their laptops and sharing the bed at night. John loved it, he wanted more, but he was happy with how things were going. He could tell that they were getting there though. Sometimes when Rodney was tired they would just snuggle. He was still waiting for their first kiss, he thought it was about time but he didn't want to push it.

Rodney was so happy, John was busier these days but they had gone with it and worked out a way round it. They sat around in the office, it had even got to the point where by the members of the science team would come looking for him in John's office before the main lab. He loved sleeping with him as well. Rodney had always been a cuddler and John despite his lankiness was a great teddy bear, as long as Rodney left his right hand free and allowed him to sleep closer to the room. John hadn't made a move on him yet though. They would sit soo close together on the couch all the time but John never made a move to kiss him or do anything else.

Rodney complained about it to Beckett next time he saw him with out John around.

"Rodney why don't you just kiss him?"

"Because, I always make the first move and every time I do he starts checking that I'm sure I want to do it. I wish he'd just trust us for once and go for it."

"Rodney, you told him at the start of all this that you weren't even interested in him. He, a man who's already lost one partner to the fact that he didn't keep close enough tabs on things. It's not surprising that he doesn't want to rush things."

"Yeah but Carson, I'm not used to this. I mean, I'm not the romantic type. I feel like everything I do isn't good enough."

"Rodney, this is your first serious relationship right?"

"Well, yes."

"Then don't be so hard on yourself. JS thinks your great, he's not going to care about any of that and if you do do it and he starts to question it again. Just tell him to shut up. If that doesn't work then point out how much thought you put into every experiment you do. You Rodney don't do anything new unless you're certain about it. I mean you still have a rant every time he goes up in one of those jumpers."

"Jumpers?"

"Yeah, JS started calling them puddle jumpers a while back. It sort of stuck. Sorry my friend but it does sound better than gateship."

"Why didn't he tell me?"

"He didn't want to hurt your feelings. Plus he knows you hate the things anyway."

"They pull him in. It worries me." Beckett just laughed at that and shooed Rodney out his infirmary as actual patients arrived.

* * *

Rodney was nervous and scared and pacing like crazy around the room. He had stayed while John went for a run. He decided to take Beckets advise and just go for it. After all, it had been announced that day that the first pregnancy had happened. Among the struggle to survive and the threat of the wraith they hadn't forgotten the primary purpose of the mission, to establish a human colony in Atlantis. In not so long people would be having kids. There were lots of marriages all ready. Rodney could see that in a few years time, this would be a home, a city with schools and families and all that stuff. He wanted to be part of that, he wanted to show John what they had both missed. First though they both needed to get over the hesitance and move some where with the relationship.

Suddenly the door opened and John walked in causing Rodney to jump a bit.

"Hey, Tense much? Just let me jump in the shower and then I'll give you a massage to help you unwind." He said with a smile pulling off his sweaty t-shirt and dumping it in the washing basket on his way to the bathroom. Rodney barely contained a frustrated groan, he just wanted to get this other with. Get the first kiss out of the way. He looked at John though and decided that actually, he could contain himself until after the SO had showered.

When the Major got out of the shower with a towel around his waist and his hair still dripping.

"John, you know how I wouldn't let you go up in the jumpers until I was sure they were safe?" He asked the man wide eyed.

"Yeah, you were worried about ancient systems." He said towelling his hair.

"Well, I don't think I would let anything happen in this relationship before I was sure it was safe for both of us." He paused then, " emotionally I mean."

"Rodney, what do you mean?" He asked putting the towel down and turning to face Rodney.

"I mean, you don't need to question this." He said stepping up to his partner and pulling him in for a kiss. JS kissed back hungrily, his arms going to encircle Rodney's waist while the scientist left his hands bearied in Johns mess of hair. It seemed like hours before they came up for air. John grinned down at Rodney.

"No question about it. Best. Kiss. Ever" Rodney grinned back and gave him another peck on the lips.

"I've been wanting to do that for so long." Rodney said, "Seriously, the tension has been killing me."

"Well, I think I can help with that tension." John murmured in a deep voice.

"Yeah, a massage was mentioned."

"Well, loose the shirt and sit on the bed. I'll just put some pants on and come join you." Rodney gave him another more lingering kiss.

"I love that I get to do that."

"Okay, down boy. We have the rest of our lives to do that." John chuckled.

"Yeah, well knowing this place that might be as long as previously assumed." Rodney grumbled, pulling his shirt over his head. John sat down behind him wearing jeans.

"Hey don't worry, I'll look after you." He wrapped his arms around his chest and leaning a head on his shoulder.

"You're wearing the jeans?" Rodney said resting his hand on his knee.

"Well, you like them. You're always more relaxed when I wear civvies. And I kind of like them." He murmured the last part into his shoulder.

"I knew you wear a jeans guy really. No one with your laid back attitude and hair could resist a good pair of jeans." Rodney said groaning in pleasure as John started the massage digging out some of the tighter knots in his shoulders.


	7. Chapter 7

**Kajos: I'm sorry for how long this chapter took. Not going to promise to update quicker, it would be a lie. I'm rubish about updating on time and won't be improving anytime soon. I'm sorry but it's the truth. I do hope you enjoy this though.**

The next morning John woke up to Rodney staring at him. He leaned in and kissed him.

"So," Rodney said carefully.

"What are you still thinking about Rodney?" John asked with a smile knowing his scientist too well.

"Well, you said you liked the jeans. Teyla and I were talking the other day and she was saying how she feels bad." JS wrinkled his forehead at that.

"Why? She's been great helping me learn her fighting style and that."

"That's why actually, she considers you a friend. She said that in her culture it's kinda like an insult to refer to someone by their initials."

"Yeah, but I don't think it is."

"She feels bad, she asked if I would mind if she called you by your first name and I said I'd talk it over with you."

"She wants to call me John? Does she realise what that means in our culture?" John said softly.

"Yes, that's why she came to ask me. She realised that calling you John was a sign that we were… we were together."

"And you would be okay with that?"

"John, you know I don't agree with the divide between military and civilians. I'm not saying I want everyone to call you John, but I wouldn't mind if your closer friends did and the rest called you Major Sheppard."

"That's not how it is though Rodney. What would people think if she started calling me John, what would they think of both of us?"

"What ever they think we will set them right. No one is going to believe that there is something going on if we're open and honest about it. We can say it is a way of respecting Teyla's people." Rodney suggested.

"Your sure you would be okay with it? I mean I wouldn't mind. Teyla isn't a civilian. So I guess it wouldn't be over familiar." John said.

"Thank you." Rodney said giving him a peck on the lips. "We can tell her together later."

"Okay." John gave him a squeeze before rolling out of bed to check his email. He kept his word and checked it every morning for anything important and a daily timetable from Ford. "looks like I'm free other than a briefing midmorning. I said I'd spare with her this afternoon. If we meet up for Lunch we can go to tell her together before we spar."

"Works for me. I have to fix some door down near the armoury then me and Zalenka are reviewing current projects for the rest of the day. He won't mind taking a long lunch." Rodney said yawning.

"Hey, why don't you have a lie in?" John said sitting back on the bed next to Rodney.

"I'm fine, we're just out of coffee and it's morning."

"Sure?"

"Yes John I'm sure. I have slept better surprisingly since we came here than I have in years thanks to someone imposing bed time on me."

"Oh, I'm sorry, I didn't realise how much you disliked cuddling up in bed with me every night. Rather than sitting on your own in a lab." John said standing up and walking over to the draws to get out some cloths for the day.

"I wasn't complaining John. I was simply pointing out that my sleep patterns… and you were just joking." He finished as John turned back to him with a smile holding one of Rodney's t-shirts. He threw it to the slightly annoyed man.

* * *

John was nervous as he walked with Rodney towards the sparing room. He gripped his partner's hand hard not sure about the decision now they were so close to Teyla.

She was already warming up when they went through the door.

"Teyla." Rodney said getting her attention.

"Yes, Rodney?" She asked making the first name mean nothing more than friendship.

"I spoke to John about your request."

"And what conclusion have to reached my friends?" She asked smiling at them both.

"We've decided that considering the differences in our cultures, it would be a great step towards us better understanding each other and being closer as peoples and as friends if you would call me, John." JS managed to say calmly to his own surprise.

"I thank you John." She said with a smile instead of the normal cringe she had when she had addressed him by name in the past. "Now, shall we proceed with our usual practise?" she asked. He turned to Rodney.

"You're going to be in my office looking over the projects with Zalenka, right?" He said.

"Yes, John, I won't be in the scary lab." He said exasperated. John leaned in and gave him a slow but gentle kiss.

"Good." He said when he broke away, before turning to warm up for the sparing.

Rodney left with a small smile and John and Teyla faced off.

"I see your relationship has progressed." Teyla commented.

"What do you mean?"

"I have not seen you exchange affection in this manner before." John blushed at that and dropped his guard for a second allowing Teyla to drop him on the mat.

"Yeah, that is new. Nice, but new."

"I have wondered for a while when you and Rodney would move on."

"It did not take _that_ long."

"John a wraith doesn't hibernate that long."

"Well, I was waiting for Rodney to be ready."

"I believe Dr McKay has been ready for some while."

"What are you saying?"

"I think perhaps you should think more on the fact that this is Rodney's first relationship. He looks to you for guidance."

"That's why I've been taking it slow."

"You misunderstand John, I think you should not be so hesitant to move on with the relationship, Rodney does not have the experience to know what ready is. You must know for him. Among my people it is expected that the one more experience in these matters will take the lead though they will of course check that their partner is still comfortable with the path they are taking."

"I never thought of it like that." John said.

* * *

The Wraith were coming. They had sent a last chance message to earth and now they were waiting for death. John sat in his office with no idea what to do; he couldn't do anything against space bombardment. He couldn't save Rodney. The door opened.

"John." The Major looked up. Rodney was stood there. He looked so lost and tired. JS stood up and went to him, pulling him into a fierce embrace. "John, I…I…"

"Shh, let's go back to our room." JS said gently wrapping his hand around the head scientists and coaxing him towards the transporter. As the door closed behind them John pulled Rodney close again and kissed him softly. "Give me a minute." He said pulling away and going to their draws. He got out his favourite casual clothing, a pair of soft jeans and one of Rodney's old t-shirts. He went back to Rodney who was sat on the bed and positioned himself behind him wrapping his arms around his waist. "Rodney, I want to have sex." He murmured into his ear.

"John, I want to, I really want to but I don't want to get pregnant in the middle of this and we don't have any protection." Rodney said sadly.

"So we do it the other way around." John said sliding a hand under his shirts to rest against his stomach. "I want you in me. Part of me."

"Why did you change if we're just going to get undressed?" Rodney laughed.

"Cause this isn't about Major JS and Dr McKay, it's about John and Rodney." Rodney thought he understood that.

"Okay." He said turning his head to kiss John. It was hotter than the one at the door with a tint of desperation. John reached up and undid the zip on Rodney's jacket and pulled it off his shoulders. They broke the kiss and threw the jacket to one side and then rushed through removing Rodney's shirt, boots and trousers. Then John lay back on the bed and pulled Rodney down with him. Rodney turned to face him as he went. "You know it's probably never going to happen now, but I wish we had time to have a family."

"Yeah, little kids with your amazing eyes and my insane hair. They would have taken over the world." Rodney chuckled at that. He stared down at the lean body beneath him and wondered how he had ended up with John, this great charming man who really cared. "You okay?" The SO asked brushing a hand against Rodney's cheek.

"Yeah, other than the whole wraith coming thing I'm really good." He said trailing his hand down John's front lightly brushing his member through the soft material of the jeans. "I think it's time these came off again." He said popping the button and pulling the zip down carefully. John burst out of the jeans. "oh god that is so sexy."

John's eyes were blown from arousal as he watched Rodney move over him naked. He grabbed Rodney pulling him down for a second fierce kiss, consuming him as between them they rid John of the denim trousers. Rodney's fingers found his hole and began to tease. John pulled back gasping at the feel of it. Rodney pushed in gently realising they really could do with some lube. "Ummm... John, do we... do we have any..."

"Yeah, Rodney." He replied, his voice raspy and a little uncomfortable. "top draw." Rodney got the tube out and smeared some on his fingers giving it a few seconds to warm up before trying again. This time John groaned at the feeling and squirmed. Rodney smiled working John loose before adding more fingers.

"We should get married." He said starring down at his SO still wearing Rodney's t-shirt.

"Not sure we have time Rodney."

"If we do survive though, we should do it. And have kids. After all we are out here to colonise and how would it look the commander of the military and the chief scientist not practising what we preach." Then Rodney brushed the nerve cluster inside of John and he let out a load gutteral moan. His head dropping back onto the pillow."Do I take that as a yes?"

"Please Rodney, more." He said when he regained speech. Rodney removed his fingers an picked up the bottle of lube. He warmed it in his hand before covering his cock. John watched panting at the sight. Rodney carefully lined himself up before he began to push in. John bit his lower lip to distract himself from the initial pain of the stretching. Once Rodney was fully sheathed they both stilled giving John time to adjust.

"You are the most amazing thing that ever happened to me. I can't believe you actually put up with me all this time."

"Nothing to put up with, Rodney. Your a great man, even if you are adorably grumpy." John whispered back giving his a gentle but deep kiss then bucking his hips to say he was ready. Rodney began to move with long slow strokes revealing his hidden strength. After a few attempts he found the spot again that caused John to loose it and started to aim for that spot with every stroke. John urged him faster with hands on his arse while Rodney began to stroke him in time with his pounding thrusts. "Oh god, Rodney. Oh god, fuck, Rodney." John murmured his head rolling back and forth on the pillow until Rodney stilled it with a kiss that fucked his mouth just as forcefully as he fucked other parts of the man. John exploded with a yell into Rodney's mouth. The scientist followed with another stroke shivering all over as he spilled himself into his SO.

* * *

They both went to sleep as soon as John had cleaned them both up. A sound sleep that was only interrupted by a profuse knocking on the door. John pulled himself out of bed with just enough sense to pull on some boxers and mentally flung the door open. "What the hell did I say about knocking on this door?" He whispered angrily at AF.

"Sir, we tried to call you on your radio's but no one answered and we need you now. Earth dialed in and sent reinforcements including a ZPM. Dr Weir wants you to speak with the Colonel that came through and she needs Dr McKay to supervise the installation of the new ZPM." JS beamed.

"Okay, for that you can knock on the door." He said enthusiastically earning a returning smile from his Lieutenant. "We'll be there as soon as possible." He closed the door and let some light into the room before going to wake Rodney up. He shook his shoulder till he blinked. "Looks like your going to have to come through on that proposal of yours last night."

"What?" Rodney groaned.

"We have reinforcements from earth, and they brought a ZPM."

"What!" Rodney said leaping up and pulling on clothing faster than John who was moving pretty god damn fast. They charged out the room a couple of minutes later and sprinted for the gate room to see a flood of Marines and stood in the middle of them was Weir speaking with a Colonel.

"Colonel, Major JS reporting, sir." John said stopping in front of them and snapping off a salute. The Colonel turned to stare at him.

"What the hell are you wearing Major?" The Colonel asked a look of disgust on his face. John looked down to see he was dressed in the clothes he had worn last night. His jeans and Rodney's t-shirt.

"Forget that, where's the damn ZPM?"

**Kajos: Well I hope you liked it. Please review that way I know it's worth carrying on with the story. There will be an update eventually can't say when though I have a busy month coming up. Thank you to all you who read this, all my reviewers, I'm sorry for technical inaccuracies.**


	8. Chapter 8

**Kajos: Hey, here's an update. Big thanks to everyones great response to the last chapter. Hope you like this one as much.**

John stepped through the gate grinning from ear to ear, his arm slung across Rodney's shoulders. He had a bag full of civvies and fully intended to get the debriefs out the way and enjoy a few days on earth with Rodney. The gate room was just how he remembered it. He looked around at the rag tag senior staff of Atlantis. The looked tired but they also looked united. As the blast doors to the left of the gate opened Dr Weir stepped forward and John straightened into a more military posture. General JO walked in accompanied by a group of SFs.

"General, it's good to see you again." Atlantis's leader said carefully eying the escort.

"Welcome back Dr Weir. I'm sorry that we have to begin your visit on such a sour note. I'm afraid I must place Major JS under arrest for neglect of duty and murder." The SFs moved towards the Major.

"What the hell?" Rodney shouted trying to step in front of John who simply held out an arm to keep him back and slowly reaching for his gun with his other hand. The SFs stopped and raised their weapons training them on him.

"Hey, calm down. I'm just going to disarm and then turn round okay?" They didn't lower their weapons but they also didn't open fire as he eased his side arm out of it's holster and knelt placing it on the ramp removing his boot knife at the same time. Then he stood up.

"John, you can't just go with them."

"I don't have a choice here, Rodney. Don't worry about me, just make sure you get some sleep okay? I'll see you soon." He turned and allowed himself to be cuffed and lead towards the door. He stopped next to the General. "Make sure he's protected. If he gets hurt I don't care what the hell the charges are or what I have to do. I will find him and help him and after that I will find you and kill you." He said before leaving the gateroom and Rodney behind, his fists clenched behind his back at that thought.

Rodney just stood there lost and aghast. John was gone. He was really gone.

"Rodney...Rodney." Elizabeth said giving him a little shake. He cringed back from the touch suddenly feeling very exposed and vulnerable.

"What?" He sounded confused so Elizabeth treated him gently.

"Rodney all we can do now is go with the General to the debriefing where I'm certain he will explain what this is all about."

Dr Jackson was sat in the briefing room clearly waiting to try and calm the Atlantis expedition after their loss. Rodney stormed in and the others followed behind slightly more restrained but no less annoyed about the events in the gate room.

"Hello, I realize you are all wanting an explanation." He said as JO moved to stand next to him. "If we could all sit down then we will do our best to tell you what is happening." They reluctantly seated themselves. JO reached over and held Daniels hand as though needing reassurance as he looked at McKay.

"Please, Dr Jackson, start talking." Dr Weir said her voice sounding as though she was straining to be diplomatic.

"The reports we received back since the start of your most recent incident were sent as is protocol to the military commanders. Particularly all reports about serious incidents resulting in deaths or injuries. It was decided based on these that Major JS was guilty of neglect of duty in allowing civilians to enter dangerous situations with out military support resulting in two deaths. Military command also doubted the report pertaining to the deaths of now two Colonels whose command he was under. We tried to call for a fair hearing considering the unknown circumstances but the decision was made and he has been found guilty on both counts. We're trying to hold of his execution with an appeal but theres not much we can do inside the military courts." Daniel spoke quickly and clearly.

"They're going to kill him!" Rodney shouted.

"Not if we can do anything about it." JO said.

"Is there any reason they might reconsider." Dr Weir said sternly.

"Well, one loophole would be that a married SO cannot be separated from his charge. The Major would still loose his command, be busted down to private most likely and be given no more privileges than those required to do his duty to his spouse but he would be free and able to return to Atlantis with you." He looked at Rodney questioningly.

"Damn it. I proposed but we decided to leave it until we got back from this trip."

"Great, there's no chance your pregnant, is there, Dr McKay?" JO drawled.

"No, General, there isn't." Rodney said through gritted teeth. Daniel put a hand on the generals arm to calm him.

"I apologizes Rodney, Jack hasn't taken this well. I think we're both fairly uncomfortable with what has happened. I know you and the Major weren't that close, or at least, you weren't but I think I speak for us both when I say the idea of having Jack taken away is my biggest nightmare."

"Danny's right, I'm just stressed, you didn't deserve that Dr McKay."

"So what are we looking at for the appeal?" Dr Weir asked.

"We're hoping to supersede the military reports with your testimony's."

"What sort of thing do you mean, laddie?" Carson asked.

"Well, if Dr Weir could explain why on occasion scientists were allowed into dangerous situations without military escorts in particular during the incident on the satellite. And if we can prove that at least the second charge of murder and use that to cast doubt on the intentions of the first murder."

"We can do that." Dr Weir said firmly. I have my report on that incident with me and I can have Atlantis transmit the video of the Colonel dieing last week. That should be fairly convincing."

"I have the medical report with me as well. I also have Rodney's medical records with me which might interest them."

"Really? What's so interesting about my medical records?"

"Since JS became your SO your blood pressure has dropped back to near normal, you haven't had an allergy attack, despite the foreign environment and food. Your caffeine intake has gone down. Your sleeping. JS is a miracle for your health." Carson listed off.

"Now, _that_ we can definitely use." Jack said pointedly at Carson.

"We have two days to put our case together in the mean time the Major is being held elsewhere, they refused to tell us where and I'm afraid you will be assigned a new SO Rodney. He's waiting for you now."

"He a good man McKay and he knows the deal, he's going to follow you around for the next couple of days, go easy on the boy." JO said standing and indicating that Rodney should follow him while Daniel took Dr Weir and Beckett else where to discus their contributions to the appeal.

Rodney followed JO reluctantly to the cafeteria. He really didn't like the idea of a different SO, even for a few days, it felt like a betrayal of John. They entered and a Major stood to attention at a table near the door.

"Dr McKay, I'd like you to meet Major EL. He will be your escort for now."

"Dr McKay." The Major said offering a hand.

"Major." He said shaking it.

"I spoke to Major JS before he shipped out. I gave him my word I would make sure you ate, slept and didn't get too wound up about this whole situation."

"You saw him? Is he okay?" Rodney suddenly interested in what the military man had to say.

"He seemed worried about you but otherwise he was calm and balanced." EL said with a small smile at the normally hostile doctors care for his SO. He was a reserve SO, he was never fully. trained as an SO but was trained in an SO unit for a period before dropping out. He had been transferred to the SGC to cover for SG personal who were killed in action or off world or otherwise incapacitated. He saw a lot of worried other halves.

"That... thats good."

"Right, well how about we head down to the labs, I believe Colonel SC wished to speak to you." He said indicating they leave through the door Rodney was still stood next to.

**Kajos: Well, I know it was short but I'm going to give you two at once to make up for it. Enjoy!**


	9. Chapter 9

**Kajos: Hello everyone! Here's a second chapter to make up for the really short first chapter. By the way there is a bit of a time jump to this chapter.**

JS's stomach felt like lead, a few years ago when he faced a similar trail he had felt ready, accepting and resigned to whatever was decided. This time he was terrified, not of death, as Rodney pointed out often he didn't value his life all that highly. He was scared of leaving Rodney alone and unprotected. He didn't think he could leave him quietly EL seemed alright but Rodney was his.

He stepped willingly through into the room in the SGC designated for the appeal. To his right say Drs Beckett and Weir. The appeal was over, due to the charges raised against him he had no right to be part of the proceedings accept to hear the verdict. In front of his sat a General and two Colonels who were his judge and jury for the day.

"We have reviewed the evidence given today and to begin with choose to refuse the request made for a second appeal to allow Dr McKay to appear. His incapacitation and continued capture is unfortunate but we must proceed."

"Permission to speak, sir?"

"Permission denied convict."

"Sir, I request an explanation of why Dr McKay can't be here."

"I said permission denied convict."

"Dr Weir?"

"There's a situation. He's stuck in the Lab. Some ancient technology was activated, no one has been able to deactivate it and they've had to seal the room to prevent the effect from spreading. No one's being allowed in or out." Dr Weir explained.

"Didn't Major EL even try?" JS demanded getting agitated.

"He does have the gene, but his expression is weaker than Rodne'ys. General JO ordered him to stand down."

"I will have order!" The General bellowed going red in the face.

"Fuck that." JS said to the General's face. He turned took out both guards without blinking. He seized a nine millimeter from one of them and exiting. He kept to the back corridors and made his way to the Labs, As he approached he saw JO stood with a squad of men at his back clearly waiting for him. He leveled his gun on the General.

"General, let me past." He said clearly.

"I can't do that." He said, the unit leveled their guns on him as well.

"I am going in to that lab, sir. I don't care what you do. I will open fire if I have to."

"We'll be forced to respond in kind."

"I'm facing death anyway. I'd rather die trying to save him than in front of the firing squad." They stared at one another for a few moments.

"Stand down." JO ordered.

"Sir?" the Sergeant to his left asked.

"He's got the strongest gene expression on base. He's our best bet for shutting off the device. Let him through." JS dropped the pistol and ran to the door opening it and rushing into the room. The door closed quickly behind him. He looked around... the room was empty.

"Rodney!" He shouted.

"I'm here, John. It's fine. I'm okay." he heard Rodney's voice through the speakers. He turned to see him sat in the observation room along with the appeal panel and Weir and Beckett. JO entered as he watched.

"Rodney?" He asked confused.

"Don't worry lad. They'll explain in a bit. Just sit tight. We'll give you and Rodney some space." Dr Beckett said as the panel filed out having seen enough.

"Rodney, you look awful. What's going on?"

"I gave my testimony earlier. There was some concerns expressed by the panel. The General suggested the panel not judge till after they had seen you in action."Rodney said quietly.

"How are you Rodney?" John begged.

"I'm okay John, I miss you."

"Your not sleeping or eating properly are you?"

"I'm trying, John, so is Lorne. But he isn't you and you know what I'm like. I get caught up in work and when Lorne brings food I'm always a little nervous about it he checks with the cooks but he doesn't check himself like you always do."

"But your trying?"

"yes."

"That's good. Tell Lorne he has my support if I can't... if I'm not able to go back to Atlantis with you."

"You will. Don't talk like that John. You have to come back, we have a wedding to go to."

John chuckled a little at that.

"We do don't we."

Rodney was called out and John was fetched from the room to return to the briefing room and hear the panels verdict for real this time.

"There are many consideration in this case. Not least of which was certain international pressures placed on us. From what we have seen and heard we judge the death of both Colonels as at the hands of the wraith. The first we consider an act of mercy and of the second you are absolved completely. Next the case of the civilians lost. We are of the opinion that you did what you could to ensure their safety. We do not believe that there were any actions you might have taken to prevent their deaths and in not sending a military escort you most likely saved military lives. So you are absolved of those charges as well.

The final consideration of this panel is your position in relation to the Atlantis mission. You have been acting commander for the past year. Though your actions during that time do not adhere to strict military protocol it must be taken in to consideration the uniqueness of your situation. The reports of the civilians leaders of the expedition are glowing as relates to you and I believe that they have suggested to the international comity that it would be good for you to remain in that position. They do not have the final say on these matters however. The military of this country has reviewed your record and decided after much debate though that we will respect their wishes. You are to be promoted to Lieutenant Colonel and made permanent Commanding Officer of Atlantis."

John couldn't believe his ears. He was not just free but he was being promoted and his position on Atlantis was being made permanent. He realized a moment later that he was being congratulated by the other leaders of the expedition.

"Rodney?" He said trying to see his Genius around everyone else.

"Here John and well done." Rodney said pushing past Beckett and giving John a hug. John held his close and tight so pleased to have him back in his arms where he could look after him.

"I love you, Rodney" He whispered in his ear and gave him a kiss on the forehead before letting him go.

"I love you too John." He said back quietly. John looked around at his... his friends who were all so pleased for him and Rodney. He couldn't wait to get home. He didn't think he would ever have one really but Atlantis was his, to protect and love just like Rodney and just like his genius he needed to get back to it.

**Kajos: Well, that's your lot. I know it took a long time coming but I really wanted to get these chapters right. Please review. Thank you for you previous ones and adds on favorite stories and alerts.** **You've been wonderful and I wish I could promise more updates but I can't. It'll be updated when it's updated I can promise to try to update as often as possible.**


	10. Chapter 10

**Kajos: Here it is at last an ending, as it should be. There was a time when I was going to write a sequel to this, or at least more of it but I'm just not up to it right now. Life has got really busy in the last year, in a good way bu it's taken me away from having time to write fanfiction. Hope you all like the ending and thanks for those of you who have held in there since the start, sorry it took so long.**

John looked around the gateroom in the evening light. I poured beautifully through the windows onto the gate and those stood by it. The soft light rippling slightly as it passed through the active gate shield. John had been a bit edgy about the standing right in the path of the vortex with out it. Dr Weir was radiant with the suns rays falling over her shoulders but John's eyes swept over her landing on the best thing he had ever seen, Rodney stood there in a dark charcoal gray suit, deep purple shirt and a simple black tie. He looked a little nervous but mostly he looked awe filled as his mouth hung open and he stared back at John in his full military dress clothes. A few steps behind him as he walked through the room was EL his new second in command after AF was lost during the siege.

He finally reach Rodney and turned to face him. Beckett nudged Rodney and he shut his mouth. John smiled a little wider. They both turned to look at Dr Weir.

"Friends we are gathered here today to join these two in matrimony. I am honored to be in the position of residing over the ceremony. These two I think you all know have not had an easy journey. Rodney has search a long time to find someone he trusts to watch his back, in JS he found someone he trusted enough to love as well. JS struggled with past mistakes and never expected a chance at this again, in Rodney he found someone he cared about enough to wait forever for. These two found each other and thanks to them we all found this place. So we respect their great efforts by witnessing their marriage here today." She said to all those gathered in the gateroom that made up their odd little Atlantian family. "Before we continue I'm required to ask if any one is aware of any reason why this marriage should not occur?" JS smiled as the silence dragged out. "Well that's good. I'm not sure what the procedure is for disposing of all the cake if the wedding doesn't happen."

"Lieutenant JS do you take Rodney, to love and to care for, to support and save, to comfort and to walk with through life, for as long as you have one another." She asked John who stood holding Rodney's hands.

"I did the first moment I saw him and I still do." He said not taking his eyes off his almost husband.

"Dr Rodney McKay do you take JS to love and to listen to, to support and share with, to comfort and walk with through life, for as long as you have one another." She asked Rodney who still looked at John with amazement in his eyes.

"Of course I do, he's wonderful." He said in his annoyed and distracted voice. John frowned at him a little and he sighed. "I do." He said simply.

"Do you, together, agree to lead with strength, work with diligence, fulfill your obligations to society and live in love for as long as you live?" They both turned to look at Elizabeth at she asked the last traditional question.

"We do." they said together. Smiling weir nodded to EL. The SO handed JS a ring, it was engraved with JS's military service number on the outside and on the inside bore the inscription 'Always here' he showed it to Rodney who swallowed and nodded in understanding before holding out his hand and letting JS slip the ring onto his finger. Weir nodded to Becket who stepped forward and held out a set of dog tags. Rodney reached forward slipping his fingers beneath JS's collar to retrieve the old set which he pulled over his head and gave to Becket taking the new set he put it over his head leaving them hanging over his shirt.

"Atlantis I give you Dr Rodney McKay and Lieutenant Colonel JM." Elizabeth announced to them all to great applause. JM pulled Rodney into a brief kiss before they turned to look at everyone else. He looked out over the smiling faces. There were babies on the way and John knew that soon he'd have kids of his own and something struck him. He didn't want to give them away. He didn't like the idea of his kids being raised by a military that saw them as numbers or in a school where they were nothing more than their IQ score. He wanted to play with them. He wanted to hold his kid in his arms and he wanted to be there for them when they had nightmares. This would have to change.

John held Rodney close that night as they recovered.

"Stop thinking so hard. It's an affront to my great skills." John chuckled at that.

"Don't worry, you did a great job. I was just thinking, Atlantis needs to declare independence." Rodney sat up swiftly.

"What?"

"I've been thinking about it for a while. What with Teyla calling me John and the military babies being stuck here with us and us. I think you and Dr Jackson might be right."

"About what exactly?" Rodney asked confused about what this whole conversation was about.

"I think we should declare independence, end segregation, though that's pretty much happened anyway, and institute a system of family care for the kids of Atlantis."

"Let me get this right... you want to make Atlantis independent, let people keep their kids if they want to and make the military part of general society? Wow, if we'd realized marrying you guys was what it took to make you see sense we'd have had this sorted ages back." John just smiled and shook his head at his astrophysicist. "How are you going to do it though?"

Twenty years later...

John put an arm around his husband who still looked just as good in his suit today as he had at their own wedding. He gazed out at the dance floor where his kids were all dancing with their partners. He couldn't have wished for more for them all. David had grown into a strong young man, an SO himself with his own husband Eli Wallace. They had a couple of little Wallaces already. Caleb was amazingly bright and though John still wasn't sure about Nick, his husband Caleb was happy and that was the most important thing. He looked over at their youngest Ella who was dancing in her wedding dress with Scot, a military marriage. He looked back again at Rodney.

"We did good didn't we?"

"Yeah, great practice for the next one." John looked at him in surprise and confusion. "I should have told you sooner, Becket told me earlier in the bathroom he got the results back this morning." John broke out in a grin.

"Do I get to tell everyone else at least?" Rodney smiled and nodded touching his stomach. John gave him a brief kiss and then stood up tapping his glass to get the attention of the room full of people.

"Hello everyone. I don't want to take anything away from my beautiful daughters special day but I have an announcement to make. Me and Rodney are going to have another kid!" There were raws of approval and their kids made a be line to them to congratulate them.

"Dad, it was supposed to be my turn next." Ella admonished Rodney.

"Hey, your only 14, you've got plenty of time to be thinking of kids Ella." John said not sure how he felt on the subject of his little girl having kids quiet yet. "Your Dad and me didn't even meet till he was 21." Ella and Rodney both rolled their eyes.

"Sir, you can't keep her forever." Caleb pointed out. All the kids call John sir and Rodney dad. But it had always been with affection.

"How are you two doing?" Rodney asked Caleb and his silent husband. John's main issue with Nick wasn't the silence. Nick was 22, Caleb was 16, he wasn't sure he liked that.

"You want to tell them?" Nick murmured in his ear.

"I'm good, you tell." They didn't sound happy though.

"We can't have kids." He said out right to them all in his thick scottish accent. "Not like you can." He looked at John and Rodney and David and Eli. "We're getting a surrogate instead."

"I'm sorry to here that, can I ask what the problem was?" John asked holding Rodney a little tighter.

"Scar tissue from an old stab wound prevents me having the surgery and Caleb can't risk it again." Caleb and Nick had lost a couple of kids already, it had been hard on the kid and the last time they had come to loosing him as well. Beckett had said they could try it the other way around but apparently that wasn't possible.

"I'm not busy tomorrow if you want some help looking for a surrogate." Rodney offered. John smiled with pride in his husband who was such a great and supportive father. He knew they would all be fine.

"Gramps, Gramps!" Jenny shouted as she held up her hands to her grandfather. Who let go of Rodney to scoop her up. "I hear you and Grandpa are having a baby, does that mean I get to be an aunt?" John laughed.

"Not quiet Jen."


	11. AN It returns

**Kajos: Hey just an authors note to say that if you liked this I have started writing a sequeal, Finding 'Family', based on John and Rodney and the struggles they go through to raise their kids. The first part, Making 'Family', has already has a chapter posted. I think this might end up being really quite long but there will be a lot of cute kids, over protective John and other great stuff. This one is being rated Teen to start with as for at least the first while there will be no funny business but the characters might get away from me after that.**


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